Cargando…
Comparative transcriptomics across the prokaryotic tree of life
Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis-antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987935/ https://www.ncbi.nlm.nih.gov/pubmed/27154273 http://dx.doi.org/10.1093/nar/gkw394 |
_version_ | 1782448373259829248 |
---|---|
author | Cohen, Ofir Doron, Shany Wurtzel, Omri Dar, Daniel Edelheit, Sarit Karunker, Iris Mick, Eran Sorek, Rotem |
author_facet | Cohen, Ofir Doron, Shany Wurtzel, Omri Dar, Daniel Edelheit, Sarit Karunker, Iris Mick, Eran Sorek, Rotem |
author_sort | Cohen, Ofir |
collection | PubMed |
description | Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis-antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of non-coding RNAs in a given organism is challenging, especially since some of these RNAs were attributed to ‘transcriptional noise’. To allow the search for conserved transcriptomic elements we produced comparative transcriptome maps for multiple species across the microbial tree of life. These transcriptome maps are detailed in annotations, comparable by gene families, and BLAST-searchable by user provided sequences. Our transcriptome collection includes 18 model organisms spanning 10 phyla/subphyla of bacteria and archaea that were sequenced using standardized RNA-seq methods. The utility of the comparative approach, as implemented in our web server, is demonstrated by highlighting genes with exceptionally long 5′UTRs across species, which correspond to many known riboswitches and further suggest novel putative regulatory elements. Our study provides a standardized reference transcriptome to major clinically and environmentally important microbial phyla. The viewer is available at http://exploration.weizmann.ac.il/TCOL, setting a framework for comparative studies of the microbial non-coding genome. |
format | Online Article Text |
id | pubmed-4987935 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-49879352016-08-22 Comparative transcriptomics across the prokaryotic tree of life Cohen, Ofir Doron, Shany Wurtzel, Omri Dar, Daniel Edelheit, Sarit Karunker, Iris Mick, Eran Sorek, Rotem Nucleic Acids Res Web Server issue Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis-antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of non-coding RNAs in a given organism is challenging, especially since some of these RNAs were attributed to ‘transcriptional noise’. To allow the search for conserved transcriptomic elements we produced comparative transcriptome maps for multiple species across the microbial tree of life. These transcriptome maps are detailed in annotations, comparable by gene families, and BLAST-searchable by user provided sequences. Our transcriptome collection includes 18 model organisms spanning 10 phyla/subphyla of bacteria and archaea that were sequenced using standardized RNA-seq methods. The utility of the comparative approach, as implemented in our web server, is demonstrated by highlighting genes with exceptionally long 5′UTRs across species, which correspond to many known riboswitches and further suggest novel putative regulatory elements. Our study provides a standardized reference transcriptome to major clinically and environmentally important microbial phyla. The viewer is available at http://exploration.weizmann.ac.il/TCOL, setting a framework for comparative studies of the microbial non-coding genome. Oxford University Press 2016-07-08 2016-05-06 /pmc/articles/PMC4987935/ /pubmed/27154273 http://dx.doi.org/10.1093/nar/gkw394 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Web Server issue Cohen, Ofir Doron, Shany Wurtzel, Omri Dar, Daniel Edelheit, Sarit Karunker, Iris Mick, Eran Sorek, Rotem Comparative transcriptomics across the prokaryotic tree of life |
title | Comparative transcriptomics across the prokaryotic tree of life |
title_full | Comparative transcriptomics across the prokaryotic tree of life |
title_fullStr | Comparative transcriptomics across the prokaryotic tree of life |
title_full_unstemmed | Comparative transcriptomics across the prokaryotic tree of life |
title_short | Comparative transcriptomics across the prokaryotic tree of life |
title_sort | comparative transcriptomics across the prokaryotic tree of life |
topic | Web Server issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987935/ https://www.ncbi.nlm.nih.gov/pubmed/27154273 http://dx.doi.org/10.1093/nar/gkw394 |
work_keys_str_mv | AT cohenofir comparativetranscriptomicsacrosstheprokaryotictreeoflife AT doronshany comparativetranscriptomicsacrosstheprokaryotictreeoflife AT wurtzelomri comparativetranscriptomicsacrosstheprokaryotictreeoflife AT dardaniel comparativetranscriptomicsacrosstheprokaryotictreeoflife AT edelheitsarit comparativetranscriptomicsacrosstheprokaryotictreeoflife AT karunkeriris comparativetranscriptomicsacrosstheprokaryotictreeoflife AT mickeran comparativetranscriptomicsacrosstheprokaryotictreeoflife AT sorekrotem comparativetranscriptomicsacrosstheprokaryotictreeoflife |